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While these breeds won’t start developing fifth legs or two tails once that level is reached, probably within the next decade, they likely will show breeding problems, lower calf survival and reduced vigor.

USDA estimates the current level of inbreeding in Holsteins and Red & Whites at 5.85%. That’s up a full percentage point from 2002 and up 1.8% from 20 years ago.

In fact, there’s already evidence of reduced reproductive efficiency. Eighteen months ago, USDA announced the discovery of five haplotypes that might cause embryo losses when animals are homozygous. Haplotypes are strings of DNA on a single chromosome that are transmitted as a unit from one generation to the next.

USDA has identified three such haplotypes in Holsteins (HH1, HH2 and HH3) and one each in Jerseys (JH1) and Brown Swiss (BH1). Homozygous animals can have a 3% to 3.7% lower conception rate, and a 1.1% to 3.7% lower rate of nonreturn at 60 days.

In smaller herds, avoiding the doubling of these haplotypes is relatively easy if the sire of the animal being bred is known. But that becomes increasingly difficult to manage as herd size increases. Just getting the right semen into the right cow can be challenging when 20 or 30 females are all synched to be bred on the same day.

To simplify sire selection for such herds, Select Sires introduced its StrataGEN program this past spring. The company has categorized five different genetic lines of Holstein sires and colored-coded them as blue, yellow, green, red and orange lines.

The idea is that a herd will use only the blue line of bulls, for example, to breed females for 18 to 21 months or so. Once the resulting heifers are of breeding age, the dairy will switch to another color code and breed exclusively to that line for the next 18 to 21 months.

"By doing that, we won’t eliminate inbreeding but we will slow the trend down," says Jeff Ziegler, genomics program manager for Select Sires.

"This program is designed for large-volume semen purchasers who do more population breeding than making distinct, individual mating decisions for each female," he says. "The program is still mass breeding, but it offers ease and simplicity from generation to generation."

Ideally, it would be good to have sire identification or genomic information on the females in the herd at the onset of the program. But simply knowing the sires of the females allows Select Sires’ analysts to make a reasoned assessment of which line of bulls to start with, Ziegler says.

One early advocate of the program was Myron Czech, vice president of the Select Sires board of directors. "The statistics show that inbreeding as a problem is getting worse and worse," he says.

Czech milks 565 registered Holsteins in Little Falls, Minn. "Inbreeding is the first thing I look at when selecting bulls, but I have a registered herd, and even with more than 500 cows, I know my individual pedigrees," he says. That’s not the case in large, commercial operations that might be made up of commingled herds or purchased heifers.

"One solution to inbreeding is crossbreeding. But a lot of people want to stay with Holsteins, so I felt we had to develop lines of bulls that are not as closely interrelated," Czech says.

One such large herd is at Ponderosa Dairy, which milks some 9,000 cows near Amargosa Valley, Nev., two hours north of Las Vegas. "We hope to get better health and reproduction, and we’re still able to make some selections within the line breeding," says Amanda Arata, general manager of the operation.

The Ponderosa Dairy herd—actually three herds including a 400-cow organic herd on one site—has been artificially bred for the past 10 to 15 years. So Arata had a pretty good idea of the sires that had been used.

It was then just a matter of working with Select Sires’ genetic specialists to pick one of the five StrataGEN lines of bulls. "We’re using about 10 different bulls from that lineup," Arata says.

"Our barn manager and herd breeder make individual matings based on whether the cow needs
udder improvement or better feet and legs," she says. "So they make a little bit of an individual evaluation on their own."

For virgin heifers, she’s selecting for calving ease and polled sires if they have equivalent genetics.

Arata started using the program last winter, so the first calves should be dropping soon. She plans to use colored ear tags to help keep the genetic lines identified.

What Competitors Say

Other AI firms offer inbreeding avoidance help in their cow mating programs. But none have gone to quite the extent of Select Sires in identifying lines of bulls that can be used against one another over time to limit inbreeding.

The main reason is that every farm is different and each represents its own genetic population, says Nate Zwald, senior director of global strategy and marketing for Alta Genetics.

"You might have to go down the line quite a ways in terms of genetic merit. In other words, you can give up genetic progress even if inbreeding might increase slightly," he says.

Genex has field programs that are user-specific and customized to the individual farm. "In some cases, it’s almost a reverse mating program—which bulls are problematic for a herd or a pen of cows," says Angie Coburn, Genex, assistant vice president of dairy genetics.

ABS Global’s Genetic Management System takes inbreeding into account through the use of recorded pedigree information, says Dan Bauer, ABS Global’s genetic programs manager. Sire recommendations are based on genetic merit.

Accelerated Genetics has a Genetic Evaluation and Mating (GEM) program that creates a RAP sheet (risk assessment profile). It develops a list of sires that are safe to use on the entire herd, based on herd history.

The program sorts bulls into three categories:

Safe to use—no breeding will result in more than 6.25% inbreeding.

Use carefully—small chance of inbreeding over 6.25% on some animals.

Use extreme care—good chance that use of these bulls will result in high inbreeding.

The level of inbreeding is reaching close to 6.25%—but breeding problems, lower calf survival and reduced vigor are already threats.